ESGEM-AMR
ESGEM-AMR Working Group
This repository is the home of the ESGEM-AMR Working Group, which focuses on curating organism-specific rule sets for interpreting AMR genotypes under the AMRrules framework.
The goal of AMRrules is to develop interpretive standards for AMR genotypes, akin to the interpretive standards developed by EUCAST and CLSI for antimicrobial susceptibility phenotyping.
An overview of the concept, with the first release of AMRrules software and rules for ESKAPEE organisms, is available in the AMRrules repository.
We have partnered with ESGEM, the ESCMID Study Group on Epidemiological Markers, to form an ESGEM-AMR Working Group to curate organism-specific rule sets.
- Slides from the introductory webinars held May 14/15 are available here.
- A detailed description of the Working Group and the overall AMRrules approach is available here, including scope, plans and timeline.
- Technical guidance for curation of rule sets is available here, this is a work in progress and will be refined as we go.
- The rule specification template is here (v0.6, under active development).
- Validated rules are available in the AMRrules repository, together with a software package to apply these rules to interpret AMRfinderplus output.
Membership
The convenors of the ESGEM-AMR Working Group are Kat Holt (LSHTM), Natacha Couto (ESGEM Chair), and Jane Hawkey (Monash, leading bioinformatics development).
A call for members was launched at the ESGEM General Meeting on April 29, 2024 and closed June 2. Over 120 applications were received and most of these have been invited to join organism-focused subgroups. We have now grown to 175 members (listed below).
Additional requests to join ESGEM-AMR will be considered periodically. In the meantime you may register your interest and let us know what organism/s you have expertise in, using this form.
[Image: Some ESGEM-AMR members attending the 2025 IMMEM XIV Conference, organised by ESGEM and ESCMID.]
Partners
We are partnering with EUCAST to ensure alignment of the AMRrules approach with the EUCAST Subcommittee on WGS and Phenotypic AST (including their first report (2017) and ongoing updates), as well as important EUCAST concepts and guidance including Expected Phenotypes, Expert Rules, wildtype distributions and ECOFFS, and Resistance Mechanisms.
We are keen to partner with other allied organisations and initiatives, please get in touch if you’d like to discuss.
Member Resources
- AMRrules Spec - v0.6 [google sheet]
- AMRrules Technical Guidance - v1.6 [PDF]
- AMRgen R package for analysing matched genotype/phenotype data [AMRgen repo]
- Code and tools for accessing public AMRfinderplus + AST data [datacuration repo]
- CARD/Antimicrobial Resistance Ontology (ARO): [browser]
- Variant specification: HGVS
- AMR rules syntax: [this repo]
- EUCAST: [Breakpoints] [Expected Resistance]
- NCBI AMRfinderplus: [software]
- NCBI refgene (AMR Gene Catalog): [browser]
- NCBI AMR Reference Gene Hierarchy: [browser] [TXT file download]
- NCBI refseq: [browser]
- NCBI AST data: [browser]
- NCBI AST data submission: [info] [submission format]
- NCBI Taxonomy: [browser]
- Introductory webinar slides: [PDF]
- Kickoff meeting slides: [PDF]
Automatic validation of rules
Before submitting rules for review, they should be first checked using the Python rulevalidator.
Member List (by subgroup)
Data & Tools - Jane Hawkey/Kat Holt, Andrew McArthur, Finlay Maguire, Michael Feldgarden, Brody Duncan, Kristy Horan, Leonid Chindelevitch, Kara Tsang, Amogelang Raphenya, Dag Harmsen, Emily Bordeleau, Mackenzie Wilke, Romain Pogorelcnik, Yu Wan, Zoe Dyson, Bogdan Iorga, Derek Sarovich, John Rossen, Silvia Argimon, Charlene Rodrigues, Rolf Kaas, Nick Duggett, Louise Teixeira Cerdeira, Matthijs Berends, Adrian Egli, João Perdigão, Tiffany Ta, Karyn Mukiri, Chiara Crestani
Enterococcus - Francesc Coll, Thomas Demuyser, Ana R. Freitas, Guido Werner, Precious Osadebamwen, Theo Gouliouris, Fiona Walsh, Valeria Bortolaia, Basil Britto Xavier, Helena Seth-Smith
Staphylococcus - Natacha Couto, Birgitta Duim, Valeria Bortolaia, Sarah Baines, Sandra Reuter, Assaf Rokney, Holly Grace Espiriu, Manal AbuOun, Sankarganesh Jeyaraj, Robert Kozak, Nick Duggett, Birgit Strommenger, Lina Cavaco, Varun Shamanna, Sabrina Di Gregorio, Teresa Ribeiro, Tim Read, Georgina Lewis-Woodhouse
Acinetobacter baumannii - Paul Higgins, Rahul Garg, Mehrad Hamidian, Bogdan Iorga, Priyanka Khopkar-Kale, Margaret Lam, Bruno Silvester Lopes, Ignasi Roca, Varun Shamanna, Clement Tsui, David Wareham, Valeria Bortolaia, Adrian Egli, Lucie Amoureux, Vera Manageiro, Antoine Abou Fayad
Enterobacter - Teresa Coque/Rafael Canton, Paul Higgins, Fernando Lazaro Perona, Po-Yu Liu, Elena Martinez, Rietie Venter, Ana Budimir, Angela Novais, Patrick Harris, Valeria Bortolaia, Val Fernandez, Vera Manageiro, Lorena Lopez Cerero
Pseudomonas aeruginosa - Antonio Oliver, Adriana Cabal Rosel, Alasdair Hubbard, Bogdan Lorga, Xena Li, Carla Lopez Causape, Juliette Severin, David Wareham, Adam Witney, Ørjan Samuelsen, Bela Kocsis, Derek Sarovich, Fernando Lazaro Perona, Valeria Bortolaia, Francesca Saluzzo, Vera Manageiro
Klebsiella pneumoniae - Kat Holt/Kara Tsang, Valeria Bortolaia, Adam Komorowski, Elisenda Miro, Jon Iredell, Ørjan Samuelsen, Sally Partridge, Manal AbuOun, Sandra Reuter, Sankarganesh Jeyaraj, Fernando Lazaro Perona, Richard Goodman, Teresa Coque, Bogdan Iorga, Clement Tsui, Margaret Lam, Priyanka Khopkar-Kale, Varun Shamanna, Adam Witney, Alasdair Hubbard, Nicole Stoesser, Sam Lipworth, Deepali Desai, Ângela Novais, Luis Gustavo Carvalho Pacheco, Iren Høyland Löhr, Daniela M Cirillo, Adrian Egli, Francesca Saluzzo, Nicholas Feasey, João Perdigão, Timothy Walsh, Oliver Pearse, Kelly Wyres, Vera Manageiro +KlebNet Geno/Pheno Consortium
Escherichia coli/Shigella - Ebenezer Foster-Nyarko Pieter-Jan Ceyssens, Fiona Walsh, Carolina Silva Nodari, Soe Yu Naing, Richard Goodman, Abdurrahman Hassan Jibril, Jelalu Kemal Birmeka, Elena Martinez, Teresa Coque, Ramon Maluping, Ana Vale, Gultekin Unal, Axel Hamprecht, Valeria Bortolaia, Bogdan Lorga, Alasdair Hubbard, Manal AbuOun, Jon Iredell, Sally Partridge, Nicole Stoesser, Sam Lipworth, Etienne Rupée, Gherard Batisti Biffignandi, Kate Baker, Adrian Egli, Timothy Walsh, Vera Manageiro, Leonor Silveira, Benjamin Parcell
Salmonella enterica - Kristy Horan/Pieter-Jan Ceyssans, Anthony Smith, Gültekin Ünal, Abdurrahman Hassan Jibril, Manal AbuOun, Jelalu Kemal Birmeka, Varun Shamanna, Assaf Rokney, Malgorzata Ligowska-Marzeta, Megan Carey, Regina Russanova, Tom Koritnik, Zoe Dyson, Leonor Silveira
Neisseria gonorrhoeae - Leonor Sanchez Buso, Yonatan Grad, Sheeba Manoharan-Basil, Martin McHugh, Tatum Mortimer, Anna Roditscheff, Faina Wehrli, Adam Witney, Raffael Frei
Mycobacterium tuberculosis - Leonid Chindelevitch, Iñaki Comas, Philip Fowler, Kristy Horan, Priyanka Khopkar-Kale, Mariana López, Conor Meehan, Adam Witney, Brian Alcock, Francesca Saluzzo, João Perdigão
Streptococcus - Mario Ramirez, Assaf Rokney, Holly Grace Espiriu, Stefanie Desmet, Elita Jauneikaite
Campylobacter - Birgitta Duim, Bruno Silvester Lopes, Malgorzata Ligowska-Marzeta, Monica Oleastro, Tee Keat Teoh, Bogdan Iorga, Diana Costa, Sangeeta Banerji, Alexandra Nunes
Haemophilus influenzae - Assaf Rokney, Charlotte Michel, Priyanka Khopkar-Kale, Derek Sarovich, Margo Diricks
Anaerobes - Trefor Morris, Ulrik Stenz Justesen, Marcela Krutova, Linda Veloo, Kathleen Boiten
Stenotrophomonas maltophilia - Jane Hawkey, Derek Sarovich, David Wareham, Fiona Walsh, Rietie Venter, Kat Holt
Serratia - Sandra Reuter, Teresa Coque, Adam Komorowski, Basil Britto Xavier, Brian Forde, João Pedro Furlan
Citrobacter- Teresa Ribeiro, Roberto Sierra, Diego Andrey
Achromobacter xylosoxidans - Charlotte Michel, Lucie Amoureux, Miglė Gabrielaitė, Lisa Påhlman
Aeromonas - Po-Yu Liu, João PedroFurlan, Hsien-Po Huang, Po-Hsiui
Shewanella - Po-Yu Liu, João PedroFurlan, Ting-Kuang Yeh
Bordetella - Laurence Luu, Carla Rodrigues
Brucella - Jelalu Kemal Birmeka
Listeria - Jelalu Kemal Birmeka, Basil Britto Xavier, Marc Lecuit, Alexandra Moura
Edwardsiella - Jelalu Kemal Birmeka
Pasteurella - Jelalu Kemal Birmeka
Burkholderia cepacia complex - Charlotte Michel, David Wareham
Burkholderia pseudomallei - Claire Chewapreecha, Derek Sarovich, Jessica Webb, Chalita Chomkatekaew
Chryseobacterium indologenes - Rietie Venter
Corynebacterium diphtheriae - Sylvain Brisse, Louise Teixeira Cerdeira, Adrian Egli, Teresa Ribeiro
Legionella - Charlotte Michel, Ghislaine Descours, Christophe Ginevra, Stefano De Giorgi, Nancy Flountzi, Sophie Jarraud
Mycoplasma - Mike Beeton, Anna Roditscheff, Sabine Pereyre, Patrick Meyer Sauteur, Nick Duggett, Jørgen Skov Jensen
Neisseria meningitidis - Célia Bettencourt, Leonor Sanchez Buso, Ala-Eddine Deghmane, Wesley Mattheus, Ana Filipa Vale, Alexandra Nunes
Proteus mirabilis - Axel Hamprecht, Janko Sattler, Elisenda Miro, Rémy Bonnin, Stephan Goettig, Shereen Shaban Abdelkareem
Treponema - Brian Alcock
Vibrio - Assaf Rokney
Yersinia - Pieter-Jan Ceyssens, Cyril Savin, Regina Russanova